I actually prefer using iBooks are my reader as well but I would use
Calibre Companion (CC) instead of OneDrive, iTunes and all the indexing you are trying to do. CC talks with caliber and you can sort various ways, book blurbs, read or not etc... and store the books on the device in CC if the files aren't too large (I use differently for comics). When you want to read something, open in iBooks and it will sync your other devices as well. Delete when finished reading, but you can always open again if needed from CC.
Inukami